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Forensic Science International: Genetics 11 (2014) 111–116

Contents lists available at ScienceDirect

Forensic Science International: Genetics


journal homepage: www.elsevier.com/locate/fsig

Forensic Population Genetics – Original Research

Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup


distribution in Pathans of Pakistan
Eun Young Lee a,1, Kyoung-Jin Shin a,1, Allah Rakha b, Jeong Eun Sim a,
Myung Jin Park a, Na Young Kim a, Woo Ick Yang a, Hwan Young Lee a,*
a
Department of Forensic Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, Republic of Korea
b
Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan

A R T I C L E I N F O A B S T R A C T

Article history: We analyzed haplotypes for 22 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/
Received 6 August 2013 b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458,
Received in revised form 3 March 2014 DYS635 and Y-GATA-H4) and five additional STRs (DYS388, DYS446, DYS447, DYS449 and DYS464), and
Accepted 4 March 2014
Y chromosomal haplogroup distribution in 270 unrelated individuals from the Pathans residing in the
Federally Administered Tribal Areas and the North-West Frontier Province of Pakistan using in-house
Keywords: multiplex PCR systems. Each Y-STR showed diversities ranging from 0.2506 to 0.8538, and the
Y chromosome
discriminatory capacity (DC) was 73.7% with 199 observed haplotypes using 17 Yfiler loci. By the
Y-STR
Haplotype
addition of 5 Y-STRs to the Yfiler system, the DC was increased to 85.2% while showing 230 observed
Haplogroup haplotypes. Among the additional 5 Y-STRs, DYS446, DYS447 and DYS449 were major contributors to
Pathans enhancing discrimination. In the analysis of molecular variance, the Pathans of this study showed
Pakistan significant differences from other Pathan populations as well as neighboring population sets. In Y-SNP
analysis, a total of 12 Y chromosomal haplogroups were observed and the most frequent haplogroup was
R1a1a with 49.3% frequency. To obtain insights on the origin of Pathans, the network analysis was
performed for the haplogroups G and Q observed from the Pathans and the Jewish population groups
including Ashkenazim and Sephardim, but little support for a Jewish origin could be found. In the present
study, we report Y-STR population data in Pathans of Pakistan, and we emphasize the need for adding
additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory
capacity in a population with low genetic diversity.
ß 2014 Elsevier Ireland Ltd. All rights reserved.

1. Introduction obtained from many studies are accessible through an online


database, YHRD (Y chromosome haplotype reference database:
Y chromosomal short tandem repeats (Y-STRs) are informative http://www.yhrd.org), which has reported 71,235 Yfiler haplotypes
markers in investigations of sexual assault, paternity and genealog- as of December, 2013 (Release 46) [7]. The database shows that Yfiler
ical tests and evolutionary studies since they are inherited paternally haplotype diversities may vary according to the genetic features of a
and their haplotype distribution may be distinct from other population; many populations have relatively high haplotype
populations of different geographic regions or with different ethnic diversity, but some populations that underwent a strong male
background [1–3]. In the field of forensics, a combination of 17 Y-STR bottleneck in their history have low haplotype diversity [8–10].
loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, Pathans are an Iranian-speaking Afghan ethnic group with a
DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, widespread geographic distribution in southern and eastern parts
DYS635 and Y-GATA-H4), the so-called Yfiler haplotype, has been of Afghanistan and in north-west Khyber Pakhtunkhwa and
commonly used to discriminate male individuals and to understand Baluchistan province of Pakistan [11,12]. Previous population
the genetic structure of populations [4–6]. Y-STR haplotypes studies on this ethnic group have revealed relatively low Y
chromosomal haplotype diversity with 17 Yfiler loci [13,14]. Since
the lack of resolution may be a challenge in its forensic application
to male lineage discrimination as well as to individual identifica-
* Corresponding author. Tel.: +82 2 2228 2482; fax: +82 2 362 0860.
tion, additional Y-STRs should be added to increase discrimination
E-mail addresses: hylee192@yuhs.ac, hylee192@gmail.com (H.Y. Lee).
1
These authors contributed equally to this work.
capacity in this population group.

http://dx.doi.org/10.1016/j.fsigen.2014.03.004
1872-4973/ß 2014 Elsevier Ireland Ltd. All rights reserved.
112 E.Y. Lee et al. / Forensic Science International: Genetics 11 (2014) 111–116

Here, we report Y chromosomal haplogroups and haplotypes for DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and
22 Y-STRs including 17 Yfiler loci and 5 additional Y-STRs (DYS388, Y-GATA-H4) and 5 additional Y-STRs (DYS388, DYS446, DYS447,
DYS446, DYS447, DYS449 and DYS464) in 270 Pathan individuals DYS449 and DYS464) were amplified using three in-house
from Pakistan, and we investigate the relationship between the multiplex PCR systems as previously described [15]. The PCR
Pathans and historically or geographically relevant populations. products were separated by capillary electrophoresis using an ABI
PRISM 310 genetic Analyzer (Applied Biosystems). A peak
2. Materials and methods detection threshold of 100 RFU was used for allele designation
using GeneMapper ID Software versions 3.2 (Applied Biosystems)
2.1. DNA samples and each allele call at all STR loci was determined by comparing to
an allelic ladder. To ensure correct allele calls, Y-STR typing results
Blood samples were obtained from 270 unrelated male Pathans for more than 100 Pathan samples and the 9948 male control DNA
residing in the North West Frontier Province (NWFP) and the (Promega Corporations, Madison, MI, USA) were confirmed to be
Federally Administered Tribal Areas (FATA) of Pakistan. All comparable with the AmpFlSTR1 YfilerTM kit (Applied Biosystems,
participants gave their informed consent orally or in writing after Foster City, CA, USA).
one of the authors explained the aims and procedures of the study,
which was approved by The Institutional Review Board of 2.3. Y chromosomal haplogroup determination
Severance Hospital, Yonsei University in Seoul, Korea. DNA was
extracted using a QIAamp DNA mini kit (Qiagen, Hilden, Germany) The 19 biallelic Y chromosomal markers (M40, RPS4Y711, M89,
according to the manufacturer’s instructions. M201, M69, M304, M172, M9, M20, M175, M122, M45, M242,
M207, P231, M17, M479, M124 and M184) were selected to
2.2. Multiplex PCR and genotyping for 22 Y-STRs determine Y chromosomal haplogroups E, C, F, G, H, J, J2, K, L, O, O3,
P, Q, R, R1, R1a1a, R2, R2a and T, that are present in Eurasian
To define genotypes of 22 Y-STRs, 17 Yfiler loci (DYS19, populations (Fig. 1). All but M172 marker that was analyzed by
DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, direct sequencing were analyzed using in-house multiplex PCR and

Fig. 1. Phylogenetic tree of the 19 Y chromosomal binary polymorphisms analyzed in this study. The SNPs are indicated in each branch and the haplogroups are indicated at
the end of each branch according to Karafet et al. [38]. The number of haplotypes of each haplogroup was compared in two different combinations of Y-STRs.
E.Y. Lee et al. / Forensic Science International: Genetics 11 (2014) 111–116 113

SBE reaction. The detailed methods for determination of Y data for 17 Yfiler loci has been deposited in the YHRD (Accession
chromosomal haplogroup are described in the Supplementary number YA003846). The locus or haplotype diversity (h) and the
Material. number of observed alleles or haplotypes for 19 single copy STR
loci and 2 multi-copy STRs are summarized in Supplementary
2.4. Statistical analysis Material Tables S2 and S3. Among single copy loci, the DYS449
showed the highest diversity of 0.8339, and the DYS388 was the
The following formulas were used: (1) discriminatory capaci- least diverse locus (h = 0.2506) with seven different alleles. The 2
ty = no. of different haplotypes/no. of individuals; (2) multi-copy Y-STRs, DYS385 and DYS464, were more diverse than
P
locus or haplotype diversity ¼ ½n=ðn  1Þ  ð1  Pi2 , where Pi most of the single copy Y-STRs with diversity values of 0.8538 and
is the frequency of the ith allele or haplotype and n indicates 0.8258, respectively.
the number of individuals [16]. To examine the relationship
between neighboring populations, pair-wise genetic distances 3.2. Haplotype resolution with additional Y-STRs
(Fst) and associated probability values (p-values, 10,000 permuta-
tions) were calculated using the analysis of molecular variance We evaluated the haplotype resolution of variously combined
(AMOVA), which is available on the YHRD website [7]. The Pathan Y-STRs (Table 1). The discriminatory capacity (DC) of the 17 Yfiler
population of the present study was compared with the loci was 73.7% with 199 different haplotypes. By the addition of 5
Afghanistan Pathans (YHRD accession number YA003701), North Y-STRs (DYS388, DYS446, DYS447, DYS449 and DYS464) to the 17
Afghanistan Pathans (YA003703), South Afghanistan Pathans Yfiler loci, an improved discrimination capacity was obtained as a
(YA003702), Afridi Pathans in India (YA003686), Yousafzai Pathans DC of 85.2% from 230 observed haplotypes in 270 Pathan samples.
in Pakistan (YA003748) and full population sets, including 483 We investigated the change in haplotype diversity (h) and DC by
haplotypes from Afghanistan [7,13,14], 2068 haplotypes from adding 5 Y-STRs to the Yfiler loci. In the case of adding one Y-STR to
India [7,10,17–19], 703 haplotypes from Iran [7,20] and 1089 the Yfiler loci, DYS449 showed the greatest increase in DC and h,
haplotypes from Pakistan [7] based on the genotyping results for which were 78.5% and 0.9939, respectively. The improvement
15 Y-STR loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, achieved by DYS449 was followed by improvements with DYS446,
DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS464 and DYS447. Since DYS449 contributed the most to
DYS635 and Y-GATA-H4). increasing haplotype diversity, we then calculated the cumulative
In addition, genealogical relationships among haplotypes of the DC and h after the addition of other Y-STR to 18 loci, including
Pathan population and Jewish populations [21,22] within hap- Yfiler loci and DYS449. The DC value increased with the addition of
logroups G and Q were reconstructed using the program Network DYS446, DYS464 and DYS447, but did not change by the addition of
4.6.1.1 [23]. Since all haplotypes overlap in only 8 Y-STR loci DYS388. When 3 loci were added to Yfiler loci, the combination of
(DYS19, DYS388, DYS389I/b, DYS390, DYS391, DYS392 and DYS446, DYS447 and DYS449 was the most effective in increasing
DYS393), the 8 loci were used for the analysis, and the weighting the discrimination capacity. The combination of 5 additional Y-
scheme took into account the Y-STR variation across the STRs with the 17 Yfiler loci increased the h and DC to 0.9968 and
haplogroup as described in a previous report [24]. AMOVA and 85.2%, respectively.
Fst analysis were also performed for haplotypes of Pathans and In addition, we examined the change in haplotype resolution
Jewish populations using Arlequin software Version 3.5.1.2 with two different combinations of Y-STR loci (Table 2). Using 17
[21,22,25]. Yfiler loci, only 169 haplotypes (62.6%) were observed once and the
most frequent haplotype was shared by 23 individuals. By adding 5
3. Results additional Y-STRs to the Yfiler loci, 211 haplotypes were observed
once, which accounted for 78.1% of the total observed haplotypes.
3.1. Diversity of 22 Y-STRs The most frequent haplotype was shared by 12 individuals, and
their unrelatedness was confirmed by the analysis of autosomal
We could successfully obtain genotypes of total 22 Y-STRs from STRs and mitochondrial DNA (mtDNA) control region sequence
270 male individuals in a Pathan population except for one (PK- (data not shown). The shared haplotypes by Yfiler loci were
164) which showed a null allele at two adjacent loci, DYS458 and separated to more distinct haplotypes by key markers, as indicated
DYS449 (Supplementary Material Table S1), and the haplotype in Supplementary Material Table S4. It was clear that the additional

Table 1
Number of haplotypes and haplotype diversities for each combined Y-STRs in 270 Pathan samples.

Haplotype Diversitya No. of haplotypes No. of unique haplotypesb Discriminatory capacity (%) Haplotype diversity

17 Yfiler loci 199 169 73.7 0.9903


Yfiler + DYS449 0.8339 212 188 78.5 0.9939
+DYS464 0.8258 210 185 77.8 0.9917
+DYS447 0.7714 203 175 75.2 0.9916
+DYS446 0.7672 211 185 78.1 0.9937
+DYS388 0.2506 200 171 74.1 0.9904
+DYS449, DYS446 222 200 82.2 0.9958
+DYS449, DYS464 219 198 81.1 0.9948
+DYS449, DYS447 217 196 80.4 0.9945
+DYS449, DYS388 212 188 78.5 0.9939
+DYS449, DYS446, DYS464 226 205 83.7 0.9964
+DYS449, DYS446, DYS447 227 208 84.1 0.9963
+DYS449, DYS447, DYS464 223 204 82.6 0.9954
+DYS449, DYS446, DYS464, DYS447 230 211 85.2 0.9968
22 Y-STRsc 230 211 85.2 0.9968
a
Locus or haplotype diversity of an added Y-STR.
b
A unique haplotype is defined as one that occurs only once in a given population according to [37] and the AmpFlSTR1 YfilerTM user’s manual.
c
22 Y-STRs: 17 Yfiler loci + DYS388, DYS446, DYS447, DYS449 and DYS464.
114 E.Y. Lee et al. / Forensic Science International: Genetics 11 (2014) 111–116

Table 2 showed significant differences from the Jewish population groups


Number of haplotypes observed in two different combinations of Y-STRs in 270 and stayed away with similar distances.
Pathan samples. In the median-joining network (MJ network) relating 49
No. of haplotypes observed Combined Y-STRs haplotypes of the G haplogroup representing 106 Y chromosomes
(Supplementary Material Fig. S2), the Pathan and the Ashkenazi
17 Yfiler loci 22 Y-STRs
Jewish populations had different dominant haplotypes from each
n=1 169 (62.6%) 211 (78.1%)
other (16–12–13–17–23–11–11–13 defined by alleles at loci in the
n=2 22 13
n=3 3 2 order DYS19, DYS388, DYS389I, DYS389b, DYS390, DYS391,
n=5 1 3 DYS392 and DYS393 for the Pathans and 15–12–14–18–23–10–
n=6 1 – 11–13 for the Ashkenazi Jews), and the Sephardic Jewish
n=7 2 – haplotypes were dispersed sporadically without core haplotype.
n = 12 – 1
n = 23 1 –
A haplotype (15–12–13–17–23–10–11–13) was observed to be
shared by a Pathan and an Ashkenazi Jew, but this haplotype was
Total 199 230 further differentiated by the addition of DYS439 (data not shown)
[21].
Within the MJ network of 16 haplotypes of the Q haplogroup
Y-STRs allowed for higher haplotype resolution. However, when representing 41 Y chromosomes (Supplementary Material Fig. S3),
haplotypes were analyzed using all 22 Y-STRs together, DYS388 did the haplotype which occupies the central position in the network
not affect the haplotype diversity because a haplotype separated was 13–12–13–16–22–10–15–13, and it was shared by 20
by DYS388 was also separated by DYS449. chromosomes from 19 Ashkenazi Jews and a Sephardic Jew. A
haplotype (13–12–13–16–22–10–15–14) shared by a Pathan and 3
3.3. Distribution of Y chromosomal haplogroups and haplotype Ashkenazi Jews was also further divided into different haplotypes
diversity within each haplogroup by the addition of DYS439 (data not shown) [21].

In Y-SNP analysis, 12 different Y chromosomal haplogroups 4. Discussion


were defined and the resultant haplogroup distribution was
mainly consistent with that of a previous study (Fig. 1 and This study demonstrated the haplotype diversity of 22 Y-STRs
Supplementary Material Table S5) [26]. The R1a1a haplogroup and its capacity to differentiate between individuals in the Pathan
with South Asian origin was observed to be the most frequent population residing in Pakistan. Seventeen loci included in the
haplogroup, with 49.3% frequency. The G haplogroup was the next Yfiler system have been commonly used for haplotype analysis
most frequent with 14.1% frequency and was followed by the J2 because their discrimination capacity was sufficiently high in most
(9.6%), R2a (7.0%) and L (5.9%) haplogroups. Every individual that populations [4–6,8]. However, some population groups such as the
shared an identical haplotype belonged to the same haplogroup Pathans were reported to have relatively low haplotype diversity
when considering 17 Yfiler loci or 22 Y-STRs. Within the R1a1a with these loci, the reason for which was assumed to be the result
haplogroup, the DC was increased to 79.7% by using 22 Y-STRs in of cultural practices like patrilocal residence and polygyny [8–10].
comparison with 65.4% by Yfiler loci. DCs within 5 haplogroups, G, With an increased number of analyzed Y-STRs, the higher
L, Q, R2a and T were also enhanced by adding Y-STR markers to the haplotype diversity can be obtained: therefore researchers have
Yfiler loci. However, haplotype resolution of J2 haplogroup was not examined various additional Y-STR loci to increase the haplotype
changed by any additional Y-STR. diversity and to improve the discriminatory capacity [8,27–29].
Therefore, in the present study, we evaluated the resolution
3.4. Population pair-wise genetic distances between neighboring capacity of five Y-STRs (DYS388, DYS446, DYS447, DYS449 and
populations DYS464) in combination with 17 Yfiler loci.
DYS449 is considered a rapidly mutating (RM) Y-STR and has
In order to analyze the relationship between the Pathans of excellent performance in male lineage discrimination in other
Pakistan and the populations residing in a neighboring regions, our studies [29,30]. RM Y-STR loci are useful in forensic work due to
population data was compared with those of neighboring Pathan their high mutation rates, which are 6.5 fold higher than Yfiler STR
populations and several population sets available in the YHRD by loci and allow differentiation between even close male relatives
calculating pair-wise genetic distances. The analyses were [29]. This character of RM Y-STRs allows for more diverse
performed with 15 loci (Supplementary Material Table S6 and genotypes, particularly in the population groups with low
Fig. S1) and there were significant differences between Pakistani haplotype resolution such as in the Pathans. DYS446 with a
Pathans and other Pathan populations from neighboring regions simple pentamer repeat motif did not stand out among various
(p < 0.05). Moreover, Pakistani Pathans did not show similarity to markers in other populations [31]. However, DYS446 did contrib-
any other population sets from neighboring areas including ute to the discrimination of more haplotypes in the Pathans despite
Afghanistan, India, Iran and Pakistan (p < 0.05). its relatively low gene diversity. This implies that haplotype
diversity is not only influenced by locus diversity of each combined
3.5. Population relationship analysis to infer the origin of Pathans Y-STR. Moreover, the value of each Y-STR should be considered in
terms of its effect on haplotype discrimination when it is combined
In order to examine correlations of genetic structural back- with others because a marker can cause a different haplotype
ground, genetic variation and distances were investigated between distribution depending on the genetic structure of a given
the Pathan population of the present study and 2 Jewish population. The most polymorphic marker was DYS464 which
populations including Ashkenazim and Sephardim [21,22] based showed 46 different haplotypes in this study. Because DYS464 is a
on the haplotype data for 8 Y-STRs, DYS19, DYS388, DYS389I/b, multi-copy STR with four positions on the Y chromosome, it can
DYS390, DYS391, DYS392 and DYS393 (Supplementary Material display various haplotypes and has high diversity. However, just
Tables S7 and S8). Of the total variance, 93.41% was resulted from like at DYS385a/b loci, it is impossible to determine the order of
differences within groups, and 6.59% was attributable to differ- alleles without additional typing of each a, b, c and d loci in
ences among the 3 population groups. The Pathan population DYS464, and thereby the diversity of DYS464 is usually
E.Y. Lee et al. / Forensic Science International: Genetics 11 (2014) 111–116 115

underestimated. Nonetheless, DYS464 shows high diversity and In addition, the high frequencies of the South Asian hap-
has been considered to be a useful discriminative marker, only that logroups, H, L, R1a1a and R2a (67.4%) and the low frequencies of
the selection of DYS464 for forensic application must be made with the Middle Eastern haplogroups G, J and T (25.2%) were not
caution since the interpretation of profiles can be ambiguous when consistent with the results of mtDNA study in the same population
it comes to male-male admixed specimens or degraded DNA group [36], where the high frequency of the West Eurasian lineages
[32,33]. In the present study, because DYS464 showed a similar (55.6%) and the relatively low frequency of the South Asian
pattern with DYS446 or DYS449 in differentiation of haplotypes, lineages (39.1%) were observed. Therefore, further analyses of
the combination of DYS464 with DYS446 or DYS449 did not other loci with more samples would be helpful to elucidate the
increase haplotype diversity despite its high diversity and the population history of the Pathans.
presence of various alleles. On the other hand, DYS447 showed a
different pattern from other loci and its addition to Yfiler loci Conflict of interest
allowed for more diverse haplotypes in spite of its low gene
diversity. The authors declare that they have no conflict of interest.
After evaluation of the usefulness of additional markers, we
selected 3 Y-STR loci, DYS446, DYS447 and DYS449, that were Acknowledgements
effective Y-STRs to increase discriminatory capacity in the Pathan
population, while DYS388 and DYS464 were excluded due to the This research was supported by the Future-based Technology
low discrimination capacity or possible difficulty in interpretation. Development Program through the National Research Foundation
The low diversity of DYS388 in Pathans has also been reported in a of Korea (NRF) funded by the Ministry of Education, Science and
previous report [9]. The combination of these 3 Y-STRs with Yfiler Technology (nos. 2010-0020631 and 2011-0027729). The authors
loci drew a DC of 84.1% which was greatly improved but still at a would like to thank Mian Sahib Zar (Center of Excellence in
lower level compared to other population data. Therefore, further Molecular Biology, University of the Punjab, Pakistan) for his
investigation into other markers is needed to achieve more valuable comments on the Pathans.
discrimination in the Pathans, and RM Y-STRs may be good
candidates since they present high differentiation capacity even in
the same male lineage [29,30]. When we compared population Appendix A. Supplementary data
differentiation, Pakistani Pathans showed a significant difference
from other Pathan populations as well as from neighboring Supplementary data associated with this article can be found, in
population sets, which suggests the need to construct their own Y- the online version, at doi:10.1016/j.fsigen.2014.03.004.
STR database.
In Y-SNP analysis, the distribution of haplogroups showed a
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